Abstract
The euphotic realm of the ocean is defined as the zone that receives enough light to allow photosynthesis. The bottom of the euphotic zone is often set as the depth at which 1 % of the incident sunlight is still available, which is in the open oligotrophic ocean approximately 200 m below the surface. In more turbid coastal waters, the euphotic zone ends at much shallower waters. Whether or not photosynthesis occurs at 1 % of the incident light intensity depends first on the actual value of the latter, on the sun angle, and not in the last place on the organism considered. Even among the same species low and high-light adapted ecotypes exist. The euphotic realm is important because it provides the primary production for the food web of the whole ocean. The microbiome of this realm is therefore characterized by microorganisms that use light. The composition of the microbiome and the ecology is intimately associated with the physicochemical characteristics of the euphotic realm.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akram N, Palovaara J, Forsberg J, Lindh MV, Milton DL, Luo H, González JM, Pinhassi J (2013) Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4. Environ Microbiol 15:1400–1415
Armbrust EV (2009) The life of diatoms in the world’s oceans. Nature 459:185–192
Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5:782–791
Beckmann A, Hense I (2007) Beneath the surface: characteristics of oceanic ecosystems under weak mixing conditions—a theoretical investigation. Prog Oceanogr 75:771–796
Béjà O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411:786–789
Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ (2013) Trichodesmium—a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol Rev 37:286–302
Borman AH, de Jong EW, Huizinga M, Kok DJ, Westbroek P, Bosch L (1982) The role in CaCO3 crystallization of an acid Ca2+-binding polysaccharide associated with coccoliths of Emiliania huxleyi. Eur J Biochem 129:179–183
Bresolin de Souza K, Jephson T, Berg Hasper T, Carlsson P (2014) Species-specific dinoflagellate vertical distribution in temperature-stratified waters. Mar Biol 161:1725–1734
Buma AGJ, van Hannen EJ, Veldhuis MJW Gieskes WWC (1996) UB-B induces DNA damage and DNA synthesis delay in the marine diatom Cyclotella sp. Sci Mar 60(suppl. 1):101–106
Buma AGJ, de Boer MK, Boelen P (2001) Depth distribution of DNA damage in Antarctic marine phyto- and bacterioplankton exposed to summertime radiation. J Phycol 37:200–208
Carlson CA, Del Giorgio PA, Herndl GJ (2008) Microbes and the dissipation of energy and respiration: from cells to ecosystems. Oceanography 20:89–100
Caron DA, Worden AZ, Countway PD, Demir E, Heidelberg KB (2009) Protists are microbes too: a perspective. ISME J 3:4–12
Cockell CS (2000) Ultraviolet radiation and the photobiology of earth’s early oceans. Orig Life Evol Biosph 30:467–499
Cullen JJ (2015) Subsurface chlorophyll maximum layers: enduring enigma or mystery solved? Annu Rev Mar Sci 7:207–239
Del Giorgio PA, Duarte CM (2002) Respiration in the open ocean. Nature 420:379–384
Deschamps P, Haferkamp I, d’Hulst C, Neuhaus HE, Ball SG (2008) The relocation of starch metabolism to chloroplasts: when, why and how. Trends Plant Sci 11:574–582
Dyhrman ST, Ammerman JW, Van Mooy BAS (2007) Microbes and the marine phosphorus cycle. Ocenography 20:110–116
Dyhrman ST, Benitez-Nelson CR, Orchard ED, Haley ST, Pellechia PJ (2009) A microbial source of phosphonates in oligotrophic marine systems. Nat Geosci 2:696–699
Eiler A (2006) Evidence for the ubiquity of mixotrophic bacteria in the upper ocean: implications and consequences. Appl Environ Microbiol 72:7431–7437
Follows MJ, Dutkiewicz S (2011) Modeling diverse communities of marine microbes. Annu Rev Mar Sci 3:427–451
Foster RA, Kuypers MMM, Vagner T, Paerl RW, Musat N, Zehr JP (2011) Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses. ISME J 5:1484–1493
Gao Q, Garcia-Pichel F (2011) Microbial ultraviolet sunscreens. Nat Rev Microbiol 9:791–802
Gattuso JP, Gentili B, Duarte CM, Kleypas JA, Middelburg JJ, Antoine D (2006) Light availability in the coastal ocean: impact on the distribution of benthic photosynthetic organisms and contribution to primary production. Biogeosciences 3:489–513
Gómez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, González JM, Pinhassi J (2010) Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol 8(4):e1000358
Hansell DA, Bates NR, Olson DB (2004) Excess nitrate and nitrogen fixation in the North Atlantic Ocean. Mar Chem 84:243–265
Herbland A, Voituriez B (1979) Hydrological structure-analysis for estimating the primary production in the tropical Atlantic Ocean. J Mar Res 37:87–101
Hess WR, Rocap G, Ting CS, Larimer F, Stilwagen S, Lamerdin J, Chisholm SW (2001) The photosynthetic apparatus of Prochlorococcus: insights through comparative genomics. Photosynth Res 70:53–71
Holm-Hansen O, Hewes CD (2004) Deep chlorophyll-a maxima (DCMs) in Antarctic waters. Polar Biol 27:699–710
Holm-Hansen O, Mitchell BG (1991) Spatial and temporal distribution of phytoplankton and primary production in the western Bransfield Strait region. Deep-Sea Res 38:961–980
Kleiner D (1985) Bacterial ammonium transport. FEMS Microbiol Rev 32:87–100
Kolber ZS, Plumley FG, Lang AS, Beatty JT, Blankenship RE, VanDover CL, Vetriani C, Koblizek M, Rathgeber C, Falkowski PG (2001) Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492–2495
Kromkamp J (1987) Formation and functional significance of storage products in cyanobacteria. NZ J Mar Freshw Res 21:457–465
Lacour L, Claustre H, Prieur L, d’Ortenzio F (2015) Phytoplankton biomass cycles in the North Atlantic subpolar gyre: a similar mechanism for two different blooms in the Labrador Sea. Geophys Res Lett 42:5403–5410
Lam P, Kuypers MMM (2011) Microbial nitrogen cycling processes in oxygen minimum zones. Annu Rev Mar Sci 3:317–345
Latifi A, Ruiz M, Zhang C-C (2009) Oxidative stress in cyanobacteria. FEMS Microbiol Rev 33:258–278
Liu X, Millero FJ (2002) The solubility of iron in seawater. Mar Chem 77:43–54
Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R, Spudich EN, Spudich JL, Béjà O (2003) Diversification and spectral tuning in marine proteorhodopsins. EMBO J 22:1725–1731
Mari X, Beauvais S, Lemée R, Pedrotti L (2001) Non-redfield C: N ratio of transparent exopolymeric particles in the northwestern Mediterranean Sea. Limnol Oceanogr 46:1831–1836
Metcalf WW, Griffin BM, Cicchillo RM, Gao J, Janga SC, Cooke HA, Circello BT, Evens BS, Martens-Habbena W, Stahl DA, van der Donk WA (2012) Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. Science 337:1104–1107
Moisander PH, Beinart RA, Hewson I, White AE, Johnson KS, Carlson DJ, Montoya JP, Zehr JP (2010) Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327:1512–1514
Moore LR, Chisholm SW (1999) Photophysiology of the marine cyanobacterium Prochlorococcus: ecotypic differences among cultured isolates. Limnol Oceanogr 44:628–638
Mulholland MR, Bernhardt PW, Blanco-Garcia JL, Mannino A, Hyde K, Mondragon E, Turk K, Moisander PH, Zehr JP (2012) Rates of dinitrogen fixation and the abundance of diazotrophs in North American coastal waters between Cape Hatteras and Georges Bank. Limnol Oceanogr 57:1067–1083
Nealson KH, Venter JC (2007) Metagenomics and the global ocean survey: what’s in it for us, and why should we care? ISME J 1:185–187
Nolting RF, Gerringa LJA, Swagerman MJW, Timmermans KR, de Baar HJW (1998) Fe (III) speciation in the high nutrient, low chlorophyll Pacific region of the Southern Ocean. Mar Chem 62:335–352
O’Brien CJ, Vogt M, Gruber N (2016) Global coccolithophore diversity: drivers and future change. Prog Oceanogr 140:27–42
Obst M, Wehrli B, Dittrich M (2009) CaCO3 nucleation by cyanobacteria: laboratory evidence for a passive, surface-induced mechanism. Geobiology 7:324–347
Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ (2011) Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75:361–422
Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14:257–263
Pedrós-Alió C (2007) Dipping into the rare biosphere. Science 315:192–193
Ploug H, Kühl M, Buchholz-Cleven B, Jørgensen BB (1997) Anoxic aggregates—an ephemeral phenomenon in the pelagic environment? Aquat Microb Ecol 13:285–294
Riebesell U, Zondervan I, Rost B, Tortell PD, Zeebe RE, Morel FMM (2000) Reduced calcification of marine plankton in response to increased atmospheric CO2. Nature 407:364–367
Riemann L, Farnelid H, Stewards GF (2010) Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters. Aquat Microb Ecol 61:235–247
Rijkenberg MJA, Fischer AC, Kroon JJ, Gerringa LJA, Timmermans KR, Wolterbeek HTh, de Baar HJW (2005) The influence of UV irradiation on the photoreduction of iron in the Southern Ocean. Mar Chem 93:119–129
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers Y-H, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5(3):e77
Santoro AE, Casciotti KL (2011) Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation. ISME J 5:1796–1808
Sass AM, Sass H, Coolen MJL, Cypionka H, Overmann J (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania Basin, Mediterranean Sea). Appl Environ Microbiol 67:5392–5402
Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F (2009) Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73:249–299
Shiba T (1991) Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst Appl Microbiol 14:140–145
Six C, Thomas J-C, Garczarek L, Ostrowski M, Dufresne A, Blot N, Scanlan DJ, Partensky F (2007) Diversity and evolution of phycobilisomes in marine Synechococcus spp.—a comparative genomics study. Genome Biol 8(12):R259
Smith RC, Prezelin BB, Baker KS, Bidigare RR, Boucher NP, Coley T, Karentz D, Macintyre S, Matlick HA, Menzies D, Ondrusek M, Wan Z, Waters KJ (1992) Ozone depletion—ultraviolet radiation and phytoplankton biology in Antarctic waters. Science 255:952–959
Stal LJ (1995) Physiological ecology of cyanobacteria in microbial mats and other communities. New Phytol 131:1–32
Stal LJ (2009) Is the distribution of nitrogen-fixing cyanobacteria in the oceans related to temperature? Environ Microbiol 11:1632–1645
Stal LJ, Walsby AE (2000) Photosynthesis and nitrogen fixation in a cyanobacterial bloom in the Baltic Sea. Eur J Phycol 35:97–108
Stomp M, Huisman J, Stal LJ, Matthijs HCP (2007a) Colourful niches of phototrophic microorganisms shaped by vibrations of the water molecule. ISME J 1:271–282
Stomp M, Huisman J, Vörös L, Pick FR, Laamanen M, Haverkamp T, Stal LJ (2007b) Colourful coexistence of red and green picocyanobacteria in lakes and seas. Ecol Lett 10:290–298
Tyrrell T (1999) The relative influences of nitrogen and phosphorus on oceanic primary production. Nature 400:525–531
van Liere L, Mur LR, Gibson CE, Herdman M (1979) Growth and physiology of Oscillatoria agardhii Gomont cultivated in continuous culture with a light-dark cycle. Arch Microbiol 123:315–318
Wagener T, Guieu C, Losno R, Bonnet S, Mahowald N (2008) Revisiting atmopsheric dust export to the Southern Hemisphere Ocean: biogeochemical implications. Glob Biogeochem Cycles GB2006 22
Wetzel RG, Hatcher PG, Bianchi TS (1995) Natural photolysis by ultraviolet irradiance of recalcitrant dissolved organic matter to simple substrates for rapid bacterial metabolism. Limnol Oceanogr 40:1369–1380
Worden AZ, Not F (2008) Ecology and diversity of picoeukaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley, NY, pp 159–205
Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE Keeling PJ (2015) Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347(6223):1257594 (1-10)
Wotton RS (2004) The ubiquity and many roles of exopolymers (EPS) in aquatic systems. Sci Mar 68:13–21
Zavarzin GA (2002) Microbial geochemical calcium cycle. Microbiology 71:1–17
Zehr JP (2011) Nitrogen fixation by marine cyanobacteria. Trends Microbiol 19:162–173
Zehr JP (2013) Interactions with partners are key for oceanic nitrogen-fixing cyanobacteria. Microbe 8:117–122
Zehr JP, Kudela RM (2011) Nitrogen cycle of the open ocean: from genes to ecosystems. Ann Rev Mar Sci 3:197–225
Acknowledgments
The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement No. 311975. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which may be made of the information contained therein.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Stal, L.J. (2016). The Euphotic Realm. In: Stal, L., Cretoiu, M. (eds) The Marine Microbiome. Springer, Cham. https://doi.org/10.1007/978-3-319-33000-6_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-33000-6_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-32998-7
Online ISBN: 978-3-319-33000-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)